Investigating molecular interactions contributing to self-assembly on ultrafast time scales with two-dimensional infrared spectroscopy

2019 Fall.Includes bibliographical references.Many chemical systems rely on π-π interactions to drive self-assembly. These systems range from peptides and proteins to polyaromatic hydrocarbons (PAH). There are a wide variety of chemical environments where π-π interactions are critically important. In such environments, factors such as sterics or the solvent surrounding these aromatic systems will affect the final aggregate. To elucidate the chemical structures and system dynamics that exist in these π stacking molecular structures, many researchers are turning their attention to examining molecular vibrations. Chemical vibrations are affected by molecular coupling, solvent environments, and aggregated state. By using infrared spectroscopy to monitor these vibrations, we can develop a molecular picture of these aggregated systems. Two-dimensional infrared (2D IR) spectroscopy provides additional information on the structure and dynamics of aggregated systems that cannot be gained from traditional linear infrared techniques. This thesis focuses on using 2D IR to study two aggregate systems. First, this thesis focuses on the self-assembly of phenylalanine based dipeptides. One of the primary goals of this work was to understand how the solvent interacts with the dipeptides, a factor critical for self-assembly. Using 2D IR and molecular dynamics simulations this work investigated how the primary structure of an aromatic dipeptide system, Val-Phe versus Phe-Val, affects the solvation dynamics around the dipeptide. It also explores the primary sequence influences hydrogen-bond dynamics. The second part of this work examines how the polarity of a solvent influences π-π stacking of PAH. Using 2D IR it was found that these solvent dependent structures have different degrees of vibrational energy delocalization. This suggests that the choice in solvent will influence the flow of energy though aggregated systems